Many things have changed in Gnome3 and with this the Network Proxy settings, actually what changed is gconf was replaced with dconf and gconf-tool-2 was replaced with gsettings. You can read more online on how to use the new one, but this is not the issue here.
The problem is many applications used gconf-tool-2 to grab the Network Proxy settings from it, one good example is Pidgin. When you try to set the Network Proxy in Gnome3 it gets set (still buggy) but old applications will not find it because it is in another place, so until applications get updated here is the temporary solution.
- Install the gconf-editor package.
- Start the gconf-editor program in gnome-terminal.
- Go to the system -> proxy tab and set the proxy you want there.
Make sure you set the mode value from “none” to manual , and for example if you want to set a socks5 proxy set the socks_host and socks_port values.
This worked fine with Pidgin, I did not test it with other applications for now.